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United States Department of Agriculture

Agricultural Research Service

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Research Project: Improved Control of Stripe Rust in Cereal Crops

Location: Wheat Genetics, Quality Physiology and Disease Research

2012 Annual Report


1a.Objectives (from AD-416):
Stripe rust is one of the most important diseases of wheat, causing significant crop losses every year throughout the world. Stripe rust of barley can cause significant yield loss in the western U.S. The long-term goal of this project is to reduce losses in wheat and barley yield and quality caused by stripe rust and assure stable, sustainable production while protecting the environment. Significant progress has been made in recent years in understanding virulence compositions of the pathogen population, identification of new sources of resistance, disease forecasting, and control of the disease using fungicides in recent years. However, more research is needed to monitor dynamic changes of virulent races, obtain better knowledge of resistance genes in elite germplasm, to identify more genes for effective resistance, and to develop molecular markers for use in the efficient incorporation of new genes into wheat and barley cultivars. For the next five years, we will conduct research to achieve the following objectives: 1). Use molecular markers and host plant responses to characterize and differentiate current and emergent virulent races of the stripe rust pathogens of wheat and barley. 2). Determine the distribution, nature, and effectiveness of host plant resistance genes amongst elite wheat and barley germplasm. 3). Identify and determine linkage relationships of new major and minor stripe rust resistance genes, and develop molecular markers for application in wheat and barley breeding efforts. Accomplishment of these objectives will lead to improved knowledge of the disease epidemiology, more resistance genes and germplasm, and more effective technology to achieve sustainable control of stripe rust.


1b.Approach (from AD-416):
Rust survey will be conducted in commercial fields, monitoring nurseries, trap plots, and experimental plots of wheat and barley, as well as wild grasses, during the plant growing-season. Rust samples will be collected by collaborators and us during rust survey. Stripe rust samples will be tested in our laboratory for race identification. New races will be tested on genetic stocks, breeding lines, and commercial cultivars to determine their danger potential. Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers will be used to characterize races and populations of the stripe rust pathogens.

All germplasm and breeding nurseries of wheat and barley will be evaluated in two locations: Pullman (eastern Washington) and Mt. Vernon (western Washington) under natural infection of the stripe rust pathogens. Uniform regional nurseries and cultivar monitoring nurseries, which include currently grown cultivars and advanced breeding lines from all U.S. regions and important stripe rust resistance stocks, will be tested with selected races at seedling stage under the low temperature profile (4-20C) and at adult-plant stage under the high temperature profile (10-30C) to determine race-specific all-stage resistance and/or non-race-specific high-temperature adult-plant resistance in wheat and barley germplasm. Stripe rust resistance genes in elite germplasm will be determined or postulated by testing elite lines, together with single resistance gene lines, with a series of races that will be selected to distinguish important genes; analyzing the pedigrees of the elite lines; testing elite lines, together with known gene lines, with molecular markers associated with particular genes; and conducting genetic studies to identify and map new genes.

To identify and map new genes for effective resistance to stripe rust in wheat. Crosses have been made with resistant germplasm lines with a susceptible line. The recombinant inbred lines of these crosses will be phenotyped for stripe rust resistance in fields and also in the greenhouse with selected races and genotyped with resistance gene analog polymorphism (RGAP), SSR, and SNP markers. The phenotypic and genotypic data will be used to map the resistance gene(s) or QTL in each cross. New genes will be identified based on their resistant types, reactions to various races, and chromosomal locations in comparison with previously reported genes.


3.Progress Report:
Progress made in the FY 2012 prior to the current project 5348-22000-015-00D initiated in March 2012 was covered in the final report for the previous project 5348-22000-014-00D which was terminated in March 2012. The progress made after March 2012 is covered in this report. Under objective 1A, we conducted intensive field surveys for monitoring stripe rust and other diseases since early spring, 2012. Rust forecasts and updates were sent to growers and the cereal crop research community. Recommendations for appropriate control measures were provided to growers as the season was progressing. As a result, the stripe rust epidemic with a potential to cause yield losses up to 40% on susceptible cultivars or up to 10% on average on all commercially grown cultivars was effectively controlled in the Pacific Northwest. We collected or received more than 500 stripe rust samples from more than 20 states. Race identification has been completed for about 300 samples. Under objective 1B, DNA was extracted for the 2011 isolates and also for more than 200 isolates of 2012. Molecular markers developed in our program have been used to characterize the isolates, and so far, about five markers are completed for the 2011 isolates. Experiments for molecular characterization of historical races in the US, together with stripe rust collections from more than 10 other countries were completed. The results revealed uniqueness and similarities between the US populations and those of other countries. We have produced more than 40 progeny isolates from a wheat stripe rust isolate through sexual reproduction on barberry and characterized them using virulence and marker tests to determine genetics of stripe rust virulence. Under objective 2, we evaluated more than 18,000 wheat and 5,000 barley lines for stripe rust resistance in the fields. We have completed data collections for all of the nurseries. Some of the nurseries were also tested in the greenhouse with selected stripe rust races. The field and greenhouse data will be used to determine if the individual lines have resistance and what types of resistance. The results will be used by breeding programs to eliminate susceptible lines, improve resistance, and release new resistant cultivars. Under objective 3, we made more than 10 crosses and tested advanced generations of four crosses for mapping new genes for stripe rust resistance in wheat. We have officially named a new gene, Yr53, in durum wheat germplasm ‘PI 480148’ from Ethiopia. We completed studies to identify and map two new genes in durum wheat genotypes ‘PI 331260’ and ‘PI 480016’. All of these genes were transferred into a common wheat background and molecular markers tightly linked to the genes were identified. In 2012, we have grown more than 500 lines developed from more than 20 crosses to select lines with different resistance genes. The genes, markers, and better plant type lines will be useful for breeding program to develop stripe rust resistant cultivars.


4.Accomplishments
1. Identified three new genes for stripe rust resistance in durum wheat and transferred the genes into common wheat. Growing resistant cultivars is the most effective, economical, and environmentally friendly approach for control of stripe rust, but new genes for effective resistance are needed to diversifying the resistance sources used in breeding programs to improve the durability of resistance in commercial cultivars. In 2012, ARS scientists from Pullman, WA, officially named Yr53, a new gene for effective all-stage resistance to stripe rust in durum wheat germplasm ‘PI 480148’ from Ethiopia, and identified and mapped two new genes in durum wheat genotypes ‘PI 331260’ and ‘PI 480016’ to the short arm of wheat chromosome 1B. All of these genes were transferred into a common wheat background and molecular markers tightly linked to the genes were identified. These new genes, associated molecular markers, and better common wheat lines carrying these genes are useful for breeding programs developing stripe rust resistant cultivars.

2. Evaluated wheat and barley germplasms and breeding lines for resistance to stripe rust. For better control of cereal rusts, it is critical to identify more germplasms and to select breeding lines of wheat and barley for resistance. During the 2012 growing season, ARS scientists from Pullman, WA, evaluated more than 18,000 wheat and 5,000 barley lines for resistance to stripe rust in the field and hundreds were also tested in the greenhouse with selected stripe rust races. From the tests, resistant germplasms were selected for further characterizing the resistance types and identifying resistance genes. The data will be used by breeding programs to select lines for releasing new cultivars with effective resistance to stripe rust.

3. Found answers for why barberry does not play an important role in stripe rust in the Pacific Northwest (PNW). Barberry has been reported to be infected by, and act as an alternate host for, the wheat stripe rust fungus under greenhouse conditions. Its role as an alternate host for the pathogen under natural conditions was not clear. ARS scientists from Pullman, WA, completed various experiments, including inoculating wheat with rust samples from barberry plants collected in the PNW, testing the samples with molecular markers distinguishing stripe rust from stem rust, determining conditions needed for the stripe rust fungus to infect barberry, and survival rates of the stripe rust fungus in comparison with the stem rust fungus. The results showed that the kind of spores from stripe rust that infect barberry cannot survive the winter under the conditions that occur in the PNW and that the infection of barberry leaves requires a minimum of 40 hours of dew formation, a weather condition that rarely occurs in the eastern PNW where barberry plants grow. These results improved our understanding of the differences in the role of barberry in the stripe rust and stem rust disease cycles; information useful to the management of these diseases.

4. Characterized virulence and molecular variations of international stripe rust collections. Wheat stripe rust occurs in many countries, but there was not much information on virulence and genetic variations on a global scale. In 2012, ARS scientists from Pullman, WA, completed a study to characterize stripe rust collections from 13 countries using virulence tests and molecular markers. Virulence to 13 resistance genes and 14 US differential wheat varieties was found in all 13 foreign countries, but also two wheat genes effective against races in all countries were identified. Comparisons using molecular markers revealed three major genetic groups, and common and unique virulence and genetic groups among countries were found. This information increases our understanding of virulence and genetic variation of the wheat stripe rust pathogen and should be useful to efforts to control the disease with stripe rust resistance throughout the world.

5. Identified races spread from the west to the east of the US. The stripe rust fungi evolve to new races and populations that damage previously resistant cultivars. To monitor the pathogen virulence changes, ARS scientists from Pullman, WA, conducted research to determined races using the wheat and barley differential varieties. In 2012, two races, PSTv-11 and PSTv-14, previously found only in the western US, were found in east of the Rocky Mountains. This result is significant as it indicates that stripe rust races can spread from the western US to the eastern US. Certain genes, such as Yr10 and YrTye, which previously were effective in the eastern US, may no longer be effective. These findings suggest that breeding programs in the eastern US should include screening for resistance to races occurring in the western US.

6. Tested fungicides for control of stripe rust. Although stripe rust can be effectively controlled by growing resistant cultivars, fungicides are still needed for reducing damage in fields grown with cultivars without an adequate level of resistance. During the 2012 growing season, ARS scientists from Pullman, WA, tested 30 fungicide treatments, including some new chemicals, for control of stripe rust. The efficacies, rates and timing of the chemicals for stripe rust control were determined. The results will be useful for the chemical developers to register new fungicides and for growers to use in disease management.


Review Publications
Wan, A., Chen, X. 2012. Virulence, frequency, and distribution of races of Puccinia striiformis f. sp. tritici and P. striiformis f. sp. hordei identified in the United States in 2008 and 2009. Plant Disease. 96:67-74.

Vazquez, M.D., Peterson, C.J., Riera-Lizarazu, O., Chen, X., Heesacker, A., Ammar, K., Crossa, J., Mundt, C.C. 2011. Genetic analysis of adult plant, quantitative resistance to stripe rust in wheat cultivar Stephens in multi-environment trials. Theoretical and Applied Genetics. 124:1-11.

Chen, J., Souza, E.J., Guttieri, M.J., O'Brien, K., Wheeler, J., Sorensen, L., Clayton, J., Chen, X., Goates, B., Hole, D., Brown, B.D., Marshall, J.M., Zemetra, R. 2011. Registration of ‘UI SRG’ wheat. Journal of Plant Registrations. 6:66-70.

Cheng, P., Chen, X., Xu, L., See, D.R. 2012. Development and characterization of expressed sequence tag-derived microsatellite markers for the wheat stripe rust fungus Puccinia striiformis f. sp. tritici. Molecular Ecology Resources. 12:779-781.

Zhan, G., Chen, X., Kang, Z., Huang, L., Wang, M., Wan, A., Cheng, P., Cao, S., Jin, S. 2012. Virulence and molecular comparison of Puccinia striiformis f. sp. tritici populations in China and the United States. Fungal Biology. 116:643-653.

Kidwell, K.K., Shelton, G.B., Demacon, V.L., Chen, X., Guy, S.O., Kuehner, J.S., Baik, B.K., Engle, D.A., Bosque-Perez, N.A. 2012. Registration of ‘Babe’ wheat. Journal of Plant Registrations. 6:156-160.

Liu, B., Chen, X., Kang, Z. 2012. Gene sequencing reveals heterokaryotic variations and evolutionary mechanisms in Puccinia striiformis. Journal of Genomics. Open Journal of Genomics.

Chen, X., Evans, C.K., Garner, J.P. 2012. Control of stripe rust of spring wheat with foliar fungicides, 2011. Plant Disease Management Reports. 6:031.

Wellings, C.R., Boyd, L.A., Chen, X. 2012. Resistance to stripe rust in wheat: Pathogen biology driving resistance breeding. Durable Disease Resistance Symposium. Sharma, I. Disease Resistance in Wheat. Edition I. New York, NY, CAB International. 63-83.

Chen, X., Evans, C.K., Garner, J.P. 2012. Control of stripe rust of winter wheat with foliar fungicides, 2011. Plant Disease Management Reports. 6:032.

Tabassum, S., Ashraf, M., Chen, X. 2010. Evaluation of Pakistan wheat germplasms for stripe rust resistance using molecular markers. Science China Life Science. 53(9):1-12.

Bux, H., Ashraf, M., Chen, X., Mumtaz, A. 2011. Effective genes for resistance to stripe rust and virulences of Puccinia striiformis f. sp. tritici in Pakistan. African Journal of Biotechnology. 10:5489-5495.

Bux, H., Ashraf, M., Chen, X. 2012. Expression of high-temperature adult-plant (HTAP) resistance against stripe rust (Puccinia striiformis f. sp. tritici) in wheat landraces. Canadian Journal of Plant Pathology. 34:68-74.

Last Modified: 10/23/2014
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